Source code for AAComposition

# -*- coding: utf-8 -*-
#  Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
#  All rights reserved.
#  This file is part of the PyBioMed.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the PyBioMed source tree.
"""
The module is used for computing the composition of amino acids, dipetide and
3-mers (tri-peptide) for a given protein sequence. You can get 8420 descriptors

for a given protein sequence. You can freely use and distribute it. If you hava

any problem, you could contact with us timely!

References
----------
.. [1] Reczko, M. and Bohr, H. (1994) The DEF data base of sequence based protein
   fold class predictions. Nucleic Acids Res, 22, 3616-3619.

.. [2] Hua, S. and Sun, Z. (2001) Support vector machine approach for protein
   subcellular localization prediction. Bioinformatics, 17, 721-728.

.. [3] Grassmann, J., Reczko, M., Suhai, S. and Edler, L. (1999) Protein fold
   class prediction: new methods of statistical classification. Proc Int Conf
   Intell Syst Mol Biol, 106-112.

Authors: Dongsheng Cao and Zhijiang Yao.

Date: 2016.7.27

Email: oriental-cds@163.com and gadsby@163.com
"""

# Core Library modules
import re

AALetter = [
    "A",
    "R",
    "N",
    "D",
    "C",
    "E",
    "Q",
    "G",
    "H",
    "I",
    "L",
    "K",
    "M",
    "F",
    "P",
    "S",
    "T",
    "W",
    "Y",
    "V",
]


#############################################################################################
def CalculateAAComposition(ProteinSequence):
    """
    ########################################################################
    Calculate the composition of Amino acids

    for a given protein sequence.

    Usage:

    result=CalculateAAComposition(protein)

    Input: protein is a pure protein sequence.

    Output: result is a dict form containing the composition of

    20 amino acids.
    ########################################################################
    """
    LengthSequence = len(ProteinSequence)
    Result = {}
    for i in AALetter:
        Result[i] = round(float(ProteinSequence.count(i)) / LengthSequence * 100, 3)
    return Result


def CalculateDipeptideComposition(ProteinSequence):
    """
    Calculate the composition of dipeptidefor a given protein sequence.

    Usage:

    result=CalculateDipeptideComposition(protein)

    Input: protein is a pure protein sequence.

    Output: result is a dict form containing the composition of

    400 dipeptides.
    """

    LengthSequence = len(ProteinSequence)
    Result = {}
    for i in AALetter:
        for j in AALetter:
            Dipeptide = i + j
            Result[Dipeptide] = round(
                float(ProteinSequence.count(Dipeptide)) / (LengthSequence - 1) * 100, 2
            )
    return Result


#############################################################################################


def Getkmers():
    """
    ########################################################################
    Get the amino acid list of 3-mers.

    Usage:

    result=Getkmers()

    Output: result is a list form containing 8000 tri-peptides.

    ########################################################################
    """
    kmers = list()
    for i in AALetter:
        for j in AALetter:
            for k in AALetter:
                kmers.append(i + j + k)
    return kmers


def GetSpectrumDict(proteinsequence):
    """
    ########################################################################
    Calcualte the spectrum descriptors of 3-mers for a given protein.

    Usage:

    result=GetSpectrumDict(protein)

    Input: protein is a pure protein sequence.

    Output: result is a dict form containing the composition values of 8000

    3-mers.
    """
    result = {}
    kmers = Getkmers()
    for i in kmers:
        result[i] = len(re.findall(i, proteinsequence))
    return result


#############################################################################################
def CalculateAADipeptideComposition(ProteinSequence):
    """
    ########################################################################
    Calculate the composition of AADs, dipeptide and 3-mers for a

    given protein sequence.

    Usage:

    result=CalculateAADipeptideComposition(protein)

    Input: protein is a pure protein sequence.

    Output: result is a dict form containing all composition values of

    AADs, dipeptide and 3-mers (8420).
    ########################################################################
    """

    result = {}
    result.update(CalculateAAComposition(ProteinSequence))
    result.update(CalculateDipeptideComposition(ProteinSequence))
    result.update(GetSpectrumDict(ProteinSequence))

    return result


#############################################################################################
if __name__ == "__main__":
    protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"

    AAC = CalculateAAComposition(protein)
    print(AAC)
    DIP = CalculateDipeptideComposition(protein)
    print(DIP)
    spectrum = GetSpectrumDict(protein)
    print(spectrum)
    res = CalculateAADipeptideComposition(protein)
    print(len(res))